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The enlargement was created by applying Excel VBA script to produce tens of (.csv) files.
Masked sequences were processed by an in-house PERL script to produce vector-free sequences.
R commands are executed through the perl cgi script to produce the image.
First, read counts were TMM normalized using a Trinity-provided Perl script to produce fragments per kilobase per million mapped expression values.
The DNA regions were aligned separately before the data were concatenated using an R [ 24] script to produce a final dataset comprising 240 taxa and 6732 nucleotides in seven DNA regions.
For this, the file New.fa, also produced during the last IMAGE iteration and containing the start and end coordinate positions of N-stretches in every scaffold, together with the scaffold sequences from Res.image.fa, were processed using a perl script to produce, for every scaffold, a multifasta file containing its contig sequences.
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Homeologous and orthologous pairs of genes defined by inter- and intraspecies comparison were merged using in-house python scripts to produce lists of pan-grass syntenic genes.
A set of utility scripts to produce a chromosome level assembly from optical map placement has been designed and is available together with the semi-automated de novo pipeline.
The word counter Perl script used to produce this number is included as a supplemental file [see Additional file 1].
This repository contains all of the datasets from Table 1, as well as the results of all analyses and the R script used to produce the figures in this manuscript.
For additional details, R scripts used to produce Figs. 4 and 5 are available as supplementary material [ 38].
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CEO of Professional Science Editing for Scientists @ prosciediting.com